% Generated by roxygen2: do not edit by hand

 % Please edit documentation in R/getBinaryMutationData.R
 \name{getBinaryMutationData}
 \alias{getBinaryMutationData}
 \title{Compute a binary gene mutation data matrix from SNP and other mutation
 event-level data.}
 \usage{

 getBinaryMutationData(
   mutInfo,
   mutData,
   maxVariantFreq = 0.2,
   maxNormalPopulationFreq = 0.005,
   maxSiftScore = 0.05,
   minPolyPhenScore = 0.85
 )

 }
 \arguments{
 \item{mutInfo}{A data frame with the following named columns:
 Gene, the name of the gene associated with the mutation event;
 probe.ids, a unique identifier specifying the mutation event;
 SNP_1000_genome, the frequency of the mutation event in SNP 1000;
 ESP5400, the frequency of the mutation event in ESP5400;

 SNP_type, the type of mutation event, chosen from "MISSENSE", "FRAMESHIFT", 

 "NONFRAMESHIFT", "NONSENSE", "SPLICING";
 SIFT_score, the SIFT score;
 Polyphen_score, the POLYPHEN score.
 Rownames of mutInfo should be set to probe.ids, i.e., the unique mutation
 event specifier.}
 
 \item{mutData}{A matrix with event level mutation information, with SNPs, etc.
 along rows and samples along columns.  Rownames of mutData should exactly
 match those of mutInfo.  The i-th row of mutInfo should thus give detailed
 information for the mutation event with data specified in the i-th row of
 mutData.}
 
 \item{maxVariantFreq}{The maximum proportion of mutant samples (used to
 exclude frequently occuring events); default value = 0.2.}
 
 \item{maxNormalPopulationFreq}{The maximum freqency of a mutation in the normal
 population (used to exclude likely germline variants); default value = 0.005.}
 

 \item{maxSiftScore}{The maximum accepted SIFT score (used to exclude 

 presumed non-deleterious mutations); default value = 0.05.}
 
 \item{minPolyPhenScore}{The minimum accepted POLYPHEN score (used to
 exclude presumed non-deleterious mutations); default value = 0.85.}
 }
 \value{
 A binary gene mutation matrix, with genes along rows, samples
 along columns, and 1s indicating deleterious mutations.
 }
 \description{
 Compute a binary gene mutation data matrix from SNP and other mutation
 event-level data.
 }

 \concept{rcellminer}